Unit 3 - Active Recall Flashcards
What are TWO types of chromosomal variations?
- Chromosome rearrangement: changes in the structure of individual chromosomes.
- Variation in chromosome numbers: changes in the
number of chromosomes. One or more individual
chromosomes are added or deleted.
What are chromosomal variations?
- Permanent chromosomal changes.
- Can be passed on to offspring if they occur in cells that will become gametes (‘germline’ cells).
Recall the four types of chromosome rearrangements?
- Deletions
- Loss of a segment, either internal or terminal, from a
chromosome.
- Arise by terminal–ends breaking off (one break) or internal breaking and rejoining of incorrect ends (two breaks).
- Major effect: loss of genetic information (importance
depends on what, and how much is lost). - Duplications
- Repetition of a chromosome segment.
- Tandem duplication is simplest form.
- Single gene or cluster of genes can be duplicated.
- Nothing has been lost, so duplications (especially smaller ones) often have little or no effect on phenotype/viability.
- Offspring with duplications usually viable.
- But, some cases, excess or unbalanced ‘dosage’ of gene products (proteins) resulting - Inversions
- Two breaks on a chromosome followed by reinsertion in the opposite orientation can produce an inversion:
i. Pericentric Inversions: span around centromere
ii. Paracentric Inversions: only on one side of chromosome - Translocation
- Exchange of segments between nonhomologous chromosomes, or to a different region on same chromosome.
- Translocations between chromosomes can be reciprocal (two-way) or non-reciprocal (one-way).
- If no genetic material is lost, considered a balanced
translocation.
Describe some consequences of deletion chromosome rearrangements and how they are detected.
Detection
- Deletion loops can be detected during meiosis
- molecular methods that detect lower heterozygosity or gene dosage
Consequences
- Loss of DNA sequences.
- Phenotypic effects depend on the size and location of deleted sequences.
- Deletions that span a centromere result in an acentric chromosome that will most likely be lost during cell division, may be lethal.
- Deletions can allow expression of alleles that are normally recessive. Called pseudodominance.
How do deletions affect gene dosage?
- When a gene is expressed, the functional protein is normally produced at the correct level or dosage.
- Some (not all) genes require two copies for normal of protein production; if one copy is deleted a mutant phenotype can result called haploinsufficiency.
Why are duplications important in evolution? What is their origin? How are they detected?
IMPORTANCE
- Very important in evolution, because extra copies of genes provide raw material for new genes and adaptations.
- About 5% of human genome consists of them
ORIGIN
- Unequal crossing over of misaligned chromosomes during meiosis generates duplications (and deletions).
DETECTION
- various molecular methods that detect higher gene dosage…staining?
What are three evolutionary outcomes of duplication?
- Both copies remain the same, Redundancy. Alter gene dosage, could have effect
- One copy becomes inactive…Pseudogene
3.One copy acquires a new function…(Neofunctionalization) Gene families
Describe the duplication consequence of neofunctionalization.
- Source of new genes
- Creates multigene families
- example: globin gene family
Describe why a duplication consequence is gene dosage?
- Gene dosage may affect phenotype.
- Amount of protein synthesized is often proportional to the number of gene copies present, so extra genes can lead to excess proteins.
- E.g., Bar region in Drosophila (X chromosome). More
copies –> fewer eye facets
Any effects of inversion of phenotype? Does location matter?
- Often, none! However, sometimes there is an effect on phenotype, driven by the change in position of the gene(s)…
- Change in position can alter expression, e.g. variegation in Drosophila.
- Genes in/near chromatin may not be expressed.
Describe the inversion consequence of suppression of recombination.
- If no crossing over occurs, gametes produced are usually viable because genetic information is not lost or gained.
- If crossing over occurs……
…outside of inverted region - viable gametes.
…within inverted region - some nonviable gametes and reduced recombination frequency.
Compare crossing over with paracentric inversion vs pericentric inversions
Paracentric inversion:
- Dicentric chromatid: Dicentric bridge breaks as the two centromeres are pulled apart
- Reduced (observed) recombination frequency
- Reduced fertility
Pericentric inversions:
- Reduced (observed) recombination frequency
- Reduced fertility
What are the consequences of reciprocal translocation?
As with inversions, translocations change the position of genes. This can alter expression of gene(s) because of association with different proteins, or formation of new gene products (fusion proteins).
Example: ‘Philadelphia’ chromosome
- Fused BCR-ABL gene
- 5’ section of BCR fused with most of ABL.
- Protein produce is a fusion that functions improperly – causes chronic myelogenous leukemia (CML), a rare form of cancer that affects certain types of WBCs
Why are inversions super interesting? Remember.
- Very interesting consequences for adaptation and evolution!
- Lack of recombination within inversions means that genes within the inversions are free to diverge to produce different adaptations.
Explain the example of Ruff Bird inversion? More than 2 sexes??
- Ruff is a European wading sandpiper.
- Has 3 types of males:
i. ‘Independent’ males display in leks to attract females.
ii. ‘Faeder’ males mimic females, sneak copulations.
iii. ‘Satellite’ males look like a somewhat drabber version of Independent males. - Faeder and satellite males have a 4.5Mb chromosomal inversion that arose 3.8 million years ago.
- Faeders came first. Later (ca 500k yr BP) a very rare crossover event restored some of the ‘independent’ version of the chromosome to the ‘faeder’ version, creating the ‘satellite’ version.
- The inversion is lethal in the homozygous condition!!
Conclusions:
- Inversion has persisted for 3.8 Million Years because being a ‘Faeder’ is a successful reproductive strategy, despite the ‘cost’ of fertilizations that are homozygous for the inversion, and therefore not viable.
- Kind of like mutation that produces sickle cell anemia in humans…beneficial effects of being heterozygous outweigh the cost of producing some offspring that are
homozygous and not viable.
Genes within alternate orientations of inversion can diverge dramatically even though there is no divergence anywhere else in the genome. Why?
- No recombination within inversion
- Sequence divergence between Independents and Satellites (also Faeders) –
- Inside inversions = large divergence
- Outside inversions = zero divergence.
- Similar cases in many other species where genes within inversions have evolved to produce different sets of
adaptations.
What do chromosomal rearrangements have to do
temperature adaptations and migratory behaviour in
Atlantic Cod?
- Cod have a large chromosomal inversion that is
millions of years old. - Genes inside the inversion influence whether cod are
adapted to ‘warmer’ or ‘colder’ water. - Cod with both orientations of the inversion live off
Nova Scotia, and interbreed. - Because recombination inside the inversion is
suppressed, the ‘warm’ and ‘cold’ versions of the
genes do not get scrambled by recombination. - Several other major inversions in cod influence other
traits, such as migration.
Recall short-term and long-term evolutionary consequences of chromosomal variations.
Short-term/immediate consequences:
- gene/chromosome dosage effects including genetic
disorders, position effects, effects on recombination & fertility (including miscarriages).
Long-term/evolutionary consequences:
- Pseudogenes, neofunctionalization, new
adaptations.
Define Aneuploidy and Polyploidy
Aneuploidy - increase or decrease in the number of individual chromosomes, e.g. trisomy, three copies of a chromosome.
Polyploidy – increase in the number of sets of chromosomes, e.g. triploid, three copies of every chromosome.
Note:
- ‘ploidy’ refers to the total number of chromosomes while ‘somy’ refers to the number of particular chromosomes
Give the four most common types of aneuploidy in diploid (2n) individuals.
- Nullisomy - Loss of both members of a pair of
homologous chromosomes: 2n-2 = 44. - Monosomy - Loss of a single chromosome: 2n-1 = 45.
- Trisomy - Gain of a single chromosome: 2n+1 = 47.
- Tetrasomy - Gain of two homologous chromosomes: 2n+2 = 48.
Note:
normal human diploid individual is 2n=46
What are the two main causes of Aneuploidy?
1) Nondisjunction in meiosis or mitosis.
- Trisomy: may be viable
- Monosomy: usually not viable, except for sex chromosomes
- chromosomal abnormalities, particularly autosomal trisomy, is thought to be the most common cause of spontaneous abortions or miscarriages.
2) Deletion of a centromere leads to chromosome loss.
Note:
Nondisjunction – failure of homologous chromosomes or sister chromatids to separate
Give examples of three autosomal aneuploidies.
- trisomy 13 Patau syndrome; about 1 in 16000
newborns - trisomy 18 Edwards syndrome; about 1 in 5000 live-
born infants - trisomy 21 Down syndrome; 1 in 800 newborns
Give four examples of Sex chromosome aneuploidies.
- monosomy X (XO)
- Turner syndrome: 1 in 2500 newborn girls
- Extra copies of the X chromosome (e.g. XXY-most common, XXXY)
- Klinefelter syndrome; 1 in 500-1000 newborn males
Describe what you know about Primary Down Syndrome? Why does the incidence of trisomy 21 rise with maternal age?
- Trisomy 21: 3 copies of chromosome 21 (2n+1 = 47 chromosomes)
- Accounts for most cases of Down syndrome.
- Most cases arise from random nondisjunction during meiotic division.
- Mother contributes the extra chromosome in ~75% of cases.
REASON:
- Possibly due to the fact that oocytes (eggs) are formed
by birth, in arrested stage of meiosis.
What is familial Down syndrome? Define Robertsonian translocation.
FAMILIAL DS:
- An extra copy of chromosome 21 is attached to another chromosome (e.g. 14 or 15).
- Account for 3-4% of cases.
- Arise in offspring of parent who carry a chromosome that underwent Robertsonian translocation
- Translocation carrier: 45 chromosomes, one of which is a translocation chromosome…Normal phenotype, does not have Down syndrome.
DEFINTION
- Robertsonian translocation = exchange of long arms of non-homologous acrocentric chromosomes
Is Aneuploidy viable in plants?
Yes! plants tolerate it better than animals.. Usually viable; phenotype maybe altered and fertility reduced.
What can you recall about polyploidy?
- For diploid (2n) individuals, polyploidy is the presence of more than two sets of chromosomes.
i. Triploids - 3n;
ii. Tetraploids - 4n;
iii. Pentaploids - 5n; and so on…… - Common in plants, less common in animals (some fishes, reptiles, amphibians and invertebrates). Not known in mammals and birds; presumably lethal.
- Polyploidy is very important in plants. 30-35% of Angiosperms evolved via some form of polyploidy.
What are the two types of polyploidy?
1) Autopolyploid: Multiples of the same genome.
e.g., autotetraploid - 4n
- can occur during mitosis or meiosis
- Nondisjunction of ALL chromosomes during mitosis in early embryo can produce autotetraploid
Ex:
- Diploid gamete + normal gamete = autotriploid (3n).
- Diploid gamete + Diploid gamete = autotetraploid (4n).
2) Allopolyploid : Multiples of closely related genomes
e.g., allotetraploid - 4n; 2n from species i and 2n from species ii
What are the effects of Autopolyploidy?
- Usually sterile (odd-numbered ploidy).
- Most gametes produced are genetically unbalanced.
What is the significance of polyploids in agriculture?
- Wheat
- cell volume correlated with nucleus volume, correlated with genome size.
- Polyploids often have bigger leaves, fruits, seeds.
- Bread wheat is a polyploid derived from 3 species. - Produce
- Production of larger fruits, e.g. strawberries and
grapes.
- Production of seedless fruit (sterile), e.g. bananas, grapes and watermelon.
Why isn’t polyploidy not the best for bananas?
- Domestic bananas (mostly 3n = 33) are derived from 2 wild species: Musa acuminata (‘A’) and Musa balbisiana (‘B’).
- ‘Gros Michel’, Cavendish are AAA
- Most plantains are ABB or AAB
- World production = 100 Mt
- Most varieties derived from spontaneous hybrid polyploids found in the wild
- 2n gametes from one species, 1n gamete
from another
Overall:
- In 1950s & 1960s, Gros Michel wiped out by ‘Panama disease’ (Fusarium)…Replaced by resistant Cavendish.
- In 1980s, a new strain of Fusarium, ‘Tropical Race 4’ appeared in Malaysia, now spreading around world. Cavendish has no resistance.
How are mutations both rare and uncommon?
- Rare because DNA replication occurs with high fidelity.
- Common because there is a lot of DNA being replicated! (e.g., ~64 new mutations/human generation)
- Ultimate source of all genetic variation.
Quickly compare somatic and gene-line mutation inheritance?
- Somatic mutations are not transmitted from one generation to another.
- Germ-line mutations may be transmitted to ~50% of offspring
What are the three types of point mutations?
- Silent (aka synonymous): no change in amino acid (aa) sequence. Happens in reading frames because of redundancy in genetic code.
- Missense (aka nonsynonymous): mutation causes 1 aa to be substituted for another, changing the aa sequence.
- Nonsense: An amino acid codon is converted into a stop codon.
What are indels? How do they affect aa sequence of protein? Do they affect phenotype?
Recall: Indels cause frameshifts that alter reading frames, creating either nonsense or missense effects on
protein….
EXCEPT when indels occur as multiples of 3 nucleotides. In such cases the amino acid sequence will change (either become shorter or longer), but the reading frame is preserved. Indels outside of reading frames
usually have no effect on phenotype.
Give some examples of mutations effect on functional phenotype?
- Loss-of-function: protein function completely or partly lost. Recessive inheritance.
- Gain-of-function (aka radical): new gene product, or gene product in ‘wrong’ tissue. Dominant inheritance.
- Neutral: Missense mutation that results in non-significant change in protein function, because one
chemically similar amino acid substituted for another, or occurs in a part of the protein that is not important for function
In point mutations, are transitions or transversions more common?
Because of the nature of the chemical changes leading to mutations, transitions are more common than transversions, even though there are twice as many possible transversions.
Classify forward and reverse mutations?
Forward mutation: alters wild phenotype
Reverse mutation changes mutant phenotype back to wild phenotype.
i. Intragenic supressor mut. (same gene)
ii. intergenic supressor mut. (Dif gene)
Note:
- Suppressor mutations: first mutation is suppressed by a second mutation
Name the three types of spontaneous mutations?
- Tautomeric shifts (base tautomers) during DNA replication.
- DNA strand-slippage during DNA replication.
- Misalignment of homologous chromosomes during
crossing-over (recombination) at meiosis I.
Mutagens are agents that cause mutations. Please give examples of RADIATION mutagens.
- Ionizing radiation: cosmic rays, X-rays and
gamma rays.
- change stable molecule into a free radical or an ion, which can alter the structure of bases and break phosphodiester bonds in DNA. - Ultraviolet radiation (from sunlight)
- Ultraviolet (UV) radiation is electromagnetic radiation of lower energy than ionizing radiation. Can still generate free radicals under some circumstances, but less likely to do so than higher energy radiation.
* Can be generated by various types of lamps, e.g., mercury vapour lamps.
- PYRIMIDINE DIMERS (TT or CC) THYMINE DIMERS INDUCED BY ULTRAVIOLET RADIATION
How does DNA repair damaged DNA?
Nucleotide excision repair:
1. Protein recognizes mismatches
2. Unwinds DNA in area of mismatch
3. Excises out nucleotides
4. Fills in correct nucleotides
Mutagens are agents that cause mutations. Please give examples of CHEMICAL mutagens.
- Base analogs.
- Chemicals that appear similar to the normal bases in DNA, but causes incorrect base-pairing and introduce point mutations during DNA replication.
- EX: 5-BROMOURACIL…A nucleotide analog that resembles both thymine and cytosine. Like thymine, 5-bromuracil normally base pairs with adenine, but when ionized it will base pair with guanine. - Base modifying agents.
- Chemicals that modify groups on the normal bases in DNA that result in incorrect base-pairing and introduce point mutations during DNA replication. - Intercalating agents.
- Chemicals that distort the normal stacking of bases in DNA resulting in insertion or deletion of a single base-pair during DNA replication.
- EX: Intercalating agents insert between adjacent bases
distorting them by 0.68 nm, the size of a base. First round of DNA replication, the DNA polymerase randomly
selects any nucleoside triphosphate opposite the
intercalating agent…Result: frame-shift due to
insertion of a base.
What is the AMES test?
Assay for chemical mutagenicity:
- A simple method to measure the reversion of a mutant His- Salmonella bacterial strain to His+ Salmonella wild-type strain by potential mutagens.
- His- Salmonella cannot grow on minimal medium lacking the essential amino acid, histidine.
- His+ Salmonella will grow on minimal medium.
- Increased reversions of His- to His+ Salmonella indicate the chemical is a mutagen, and thus, a potential carcinogen.
Note:
- Inclusion of rat liver enzymes to mimic the chemical modification of potential mutagens in the human body.
- Liver enzymes could make the chemical more or less
mutagenic.
Define Type 1 restriction endonucleases
- Type I restriction endonucleases, discovered in
1960s, recognize specific DNA sequences and then cleave the DNA sequences…somewhere else. - “Restrict” entry of foreign (i.e., viral) DNA into bacterial cells.
- Originally thought to be rare, later found to be very common.
- not very useful in molecular biology.
Define Type 2 restriction endonucleases (aka restriction enzymes).
- First reported in 1970.
- Thousands now known, hundreds commercially
available. - ‘Type II’ REs cleave DNA within the recognition site.
- This property has made them incredibly useful in
molecular biology.
Define a palindromic sequence?
Sequence of nucleotide bases reads the same on the top strand as the sequence of nucleotide bases reads on the bottom strand of the DNA molecule in 5′ - 3’ direction.
Ex:
5’ - GAATTC - 3’
3’ - CTTAAG - 5’
Why don’t bacterial restriction endonucleases
attack the host’s own DNA?
The most common reason is that the ‘host’ (bacterial cell)
methylates a base in every copy of the RE site within its own genome.
Note: When we get to CRISPR we will encounter an even more clever bacterial host defence system.
DNA sequences cut by Type II restriction
endonucleases can be rejoined with _______.
ligases
Gel electrophoresis..What do you recall about this?
- a method for sorting DNA (& RNA) sequence fragments by size
- At neutral pH, DNA molecules are negatively charged because of phosphate groups.
- In an electrical field, DNA will tend to move toward
the positive electrode. - In addition to agarose and water, the gel contains a buffer that provide ions to allow current flow, and to keep the pH slightly above neutral.
Why can’t electrophoresis be done in a liquid?
Cannot do electrophoresis in a liquid. Need to make a ‘gel’. Most common kind is made from agarose, an uncharged polysaccharide purified from agar of the seaweed, Agar agar.
